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Fulltext Draft Genome Sequence of Dematiaceous Coelomycete Pyrenochaeta sp. Strain UM 256, Isolated from Skin Scraping

Yew SM, Chan CL, Soo-Hoo TS, Na SL, Ong SS, Hassan H, et al.

Genome Announc, 2013;1(3).
PMID: 23723391 DOI: 10.1128/genomeA.00158-13

Pyrenochaeta, classified under the order Pleosporales, is known to cause diseases in plants and humans. Here, we report a draft genome sequence of a Pyrenochaeta sp. isolated from a skin scraping, with an estimated genome size of 39.4 Mb. Genes associated with the synthesis of proteases, toxins, plant cell wall degradation, and multidrug resistance were found.
Fulltext Draft Genome Sequence of Herpotrichiellaceae sp. UM 238 Isolated from Human Skin Scraping

Ng KP, Yew SM, Chan CL, Tan R, Soo-Hoo TS, Na SL, et al.

Genome Announc, 2013 Jan;1(1).
PMID: 23409267 DOI: 10.1128/genomeA.00148-12

Herpotrichiellaceae spp. are known to be opportunistic human pathogens. Here, we report the ~28.46-Mb draft genome of Herpotrichiellaceae sp. UM 238, isolated from human skin scraping. The UM 238 genome was found to contain many classes of protective genes that are responsible for fungal adaptation under adverse environmental conditions.
Fulltext Draft Genome Sequence of Ochroconis constricta UM 578, Isolated from Human Skin Scraping

Chan CL, Yew SM, Na SL, Tan YC, Lee KW, Yee WY, et al.

Genome Announc, 2014;2(2).
PMID: 24744321 DOI: 10.1128/genomeA.00074-14

Ochroconis constricta is a soilborne dematiaceous fungus that has never been reported to be associated with human infection. Here we report the first draft genome sequence of strain UM 578, isolated from human skin scraping. The genomic information revealed will contribute to a better understanding of this species.
Fulltext Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia

Ng KP, Yew SM, Chan CL, Chong J, Tang SN, Soo-Hoo TS, et al.

Genome Announc, 2013 Jan;1(1).
PMID: 23405310 DOI: 10.1128/genomeA.00056-12

The emergence of the global threat of extensively drug-resistant (XDR) Mycobacterium tuberculosis reveals weaknesses in tuberculosis management and diagnostic services. We report the draft genome sequence of the first extensively drug-resistant Mycobacterium tuberculosis strain isolated in Malaysia. The sequence was also compared against a reference strain to elucidate the polymorphism that is related to their extensive resistance.
Fulltext Draft genome sequence of Daldinia eschscholzii isolated from blood culture

Ng KP, Ngeow YF, Yew SM, Hassan H, Soo-Hoo TS, Na SL, et al.

Eukaryotic Cell, 2012 May;11(5):703-4.
PMID: 22544898 DOI: 10.1128/EC.00074-12

Daldinia eschscholzii is an invasive endophyte that is most commonly found in plant tissues rich in secondary metabolites. We report the draft genome sequence of D. eschscholzii isolated from blood culture. The draft genome is 35,494,957 bp in length, with 42,898,665 reads, 61,449 contigs, and a G+C content of 46.8%. The genome was found to contain a high abundance of genes associated with plant cell wall degradation enzymes, mycotoxin production, and antifungal drug resistance.
Fulltext Draft genome sequence of Mycobacterium bolletii strain M24, a rapidly growing mycobacterium of contentious taxonomic status

Wong YL, Choo SW, Tan JL, Ong CS, Ng KP, Ngeow YF

J Bacteriol, 2012 Aug;194(16):4475.
PMID: 22843600 DOI: 10.1128/JB.00916-12

The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar lavage fluid of a Malaysian patient, is reported here. The circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of this organism within the M. abscessus complex and revealed the presence of proteins potentially important for pathogenicity in a human host.
Emergence of HIV-1 CRF01_AE/B unique recombinant forms in Kuala Lumpur, Malaysia

Tee KK, Pon CK, Kamarulzaman A, Ng KP

AIDS, 2005 Jan 28;19(2):119-26.
PMID: 15668536

OBJECTIVES: To investigate the molecular epidemiology of HIV-1 and to screen for the emergence of intersubtype recombinants in Kuala Lumpur, Malaysia.
DESIGN: A molecular epidemiology study was conducted among HIV-1 seropositive patients attending the University Malaya Medical Center (UMMC) from July 2003 to June 2004.
METHODS: Protease (PR) and reverse transcriptase (RT) gene sequences were derived from drug resistance genotyping assay of 100 newly diagnosed or antiretroviral-naive patients. These were phylogenetically analysed to determine the subtypes and recombination breakpoint analyses were performed on intersubtype recombinants to estimate the recombination breakpoint(s).
RESULTS: CRF01_AE predominated in Kuala Lumpur with 65% in both PR and RT genes. B subtype was detected at 14% and 12% in PR and RT genes, respectively. C subtype was present at 1% in both genes. Overall, the concordance of PR and RT genes in discriminating subtypes/circulating recombinant forms (CRF) was high at 96%. In this study, novel CRF01_AE/B intersubtype recombinants were detected at high prevalence (22%), including those isolates with subtype discordance. Thai variants of CRF01_AE and B subtype were involved in the genesis of these unique recombinant forms (URF). Interestingly, 19 CRF01_AE/B intersubtype recombinant isolates shared similar recombination breakpoints in both PR and RT genes. Several distinct URF were also identified.
CONCLUSION: PR and RT genes can be utilized for subtype/CRF assessment with high degree of agreement, allowing concurrent surveillance of circulating HIV-1 subtypes with antiretroviral drug resistance genotyping tests. The emergence of highly identical CRF01_AE/B intersubtype recombinants suggests the possibility of the appearance of a new circulating recombinant form in Kuala Lumpur.
Fulltext Estimating renal function in the elderly Malaysian patients attending medical outpatient clinic: a comparison between creatinine-based and cystatin-C based equations

Jalalonmuhali M, Elagel SMA, Tan MP, Lim SK, Ng KP

Int J Nephrol, 2018;2018:3081518.
PMID: 29862077 DOI: 10.1155/2018/3081518

Background: To assess the performance of different GFR estimating equations, test the diagnostic value of serum cystatin-C, and compare the applicability of cystatin-C based equation with serum creatinine based equation for estimating GFR (eGFR) in comparison with measured GFR in the elderly Malaysian patients.

Methods: A cross-sectional study recruiting volunteered patients 65 years and older attending medical outpatient clinic. 51 chromium EDTA (51Cr-EDTA) was used as measured GFR. The predictive capabilities of Cockcroft-Gault equation corrected for body surface area (CGBSA), four-variable Modification of Diet in Renal Disease (4-MDRD), and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations using serum creatinine (CKD-EPIcr) as well as serum cystatin-C (CKD-EPIcys) were calculated.

Results: A total of 40 patients, 77.5% male, with mean measured GFR 41.2 ± 18.9 ml/min/1.73 m2 were enrolled. Mean bias was the smallest for 4-MDRD; meanwhile, CKD-EPIcr had the highest precision and accuracy with lower limit of agreement among other equations. CKD-EPIcys equation did not show any improvement in GFR estimation in comparison to CKD-EPIcr and MDRD.

Conclusion: The CKD-EPIcr formula appears to be more accurate and correlates better with measured GFR in this cohort of elderly patients.

Study site: medical outpatient clinic. University of Malaya Medical Centre (UMMC)
Etiology of blood culture isolates among patients in a multidisciplinary teaching hospital in Kuala Lumpur

Karunakaran R, Raja NS, Ng KP, Navaratnam P

J Microbiol Immunol Infect, 2007 Oct;40(5):432-7.
PMID: 17932604

Bloodstream infections are an important cause of morbidity and mortality among hospitalized patients and the surveillance of etiological agents in these infections is important for their prevention and treatment. Data on common organisms isolated from blood cultures from Malaysia are limited, and our aim was to identify the common bloodstream isolates in hospitalized patients at the University of Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia.
Fulltext Evaluation of Elecsys Syphilis Assay for Routine and Blood Screening and Detection of Early Infection

Kremastinou J, Polymerou V, Lavranos D, Aranda Arrufat A, Harwood J, Martínez Lorenzo MJ, et al.

J Clin Microbiol, 2016 09;54(9):2330-6.
PMID: 27358468 DOI: 10.1128/JCM.02544-15

Treponema pallidum infections can have severe complications if not diagnosed and treated at an early stage. Screening and diagnosis of syphilis require assays with high specificity and sensitivity. The Elecsys Syphilis assay is an automated treponemal immunoassay for the detection of antibodies against T. pallidum The performance of this assay was investigated previously in a multicenter study. The current study expands on that evaluation in a variety of diagnostic settings and patient populations, at seven independent laboratories. The samples included routine diagnostic samples, blood donation samples, samples from patients with confirmed HIV infections, samples from living organ or bone marrow donors, and banked samples, including samples previously confirmed as syphilis positive. This study also investigated the seroconversion sensitivity of the assay. With a total of 1,965 syphilis-negative routine diagnostic samples and 5,792 syphilis-negative samples collected from blood donations, the Elecsys Syphilis assay had specificity values of 99.85% and 99.86%, respectively. With 333 samples previously identified as syphilis positive, the sensitivity was 100% regardless of disease stage. The assay also showed 100% sensitivity and specificity with samples from 69 patients coinfected with HIV. The Elecsys Syphilis assay detected infection in the same bleed or earlier, compared with comparator assays, in a set of sequential samples from a patient with primary syphilis. In archived serial blood samples collected from 14 patients with direct diagnoses of primary syphilis, the Elecsys Syphilis assay detected T. pallidum antibodies for 3 patients for whom antibodies were not detected with the Architect Syphilis TP assay, indicating a trend for earlier detection of infection, which may have the potential to shorten the time between infection and reactive screening test results.
Evaluation of a rapid test for the detection of antibodies to human immunodeficiency virus type 1 and 2

Ng KP, Saw TL, Baki A, He J, Singh N, Lyles CM

Int J STD AIDS, 1999 Jun;10(6):401-4.
PMID: 10414883

Hema-Strip HIV-1/2 is a one-step rapid test for the detection of anti-HIV-1/2 antibodies in whole blood. The test requires no expensive equipment and the results are available within 10-15 min. Using 72 known HIV-1 positive samples and 780 high-risk prisoners, the sensitivity and specificity of Hema-Strip HIV-1/2 was found to be comparable to microparticle enzyme immunoassay (MEIA). The data also indicated that Hema-Strip HIV-1/2 is an effective alternate testing system to conventional ELISA where the use of ELISA is not suitable and the result of the HIV testing is needed urgently.
Fulltext Evaluation of three commercial rapid tests for detecting antibodies to human immunodeficiency virus

Ng KP, Saw TL, Baki A, Kamarudin R

Med J Malaysia, 2003 Aug;58(3):454-60.
PMID: 14750391

Determine HIV-1/2, Chembio HIV-1/2 STAT-PAK and PenTest are simple/rapid tests for the detection of antibodies to HIV-1 and HIV-2 in human whole blood, serum and plasma samples. The assay is one step and the result is read visually within 15 minutes. Using 92 known HIV-1 reactive sera and 108 known HIV-1 negative sera, the 3 HIV tests correctly identified all the known HIV-1 reactive and negative samples. The results indicated that Determine HIV-1/2, Chembio HIV-1/2 STAT-PAK and PenTest HIV are as sensitive and specific (100% concordance) as Microparticle Enzyme Immunoassay. The data indicated that these 3 HIV tests are effective testing systems for diagnosis of HIV infection in a situation when the conventional Enzyme Immunoassay is not suitable.
Evidence for possible biological advantages of the newly emerging HIV-1 circulating recombinant form from Malaysia - CRF33_01B in comparison to its progenitors - CRF01_AE and subtype B

Lau KA, Wang B, Miranda-Saksena M, Boadle R, Kamarulzaman A, Ng KP, et al.

Curr. HIV Res., 2010 Apr;8(3):259-71.
PMID: 20214658

In Malaysia, co-circulation of CRF01_AE and subtype B has resulted in the emergence of the second generation derivative; CRF33_01B in approximately 20% of its HIV-1 infected individuals. Our objective was to identify possible biological advantages that CRF33_01B possesses over its progenitors. Biological and molecular comparisons of CRF33_01B against its parental subtypes clearly show that CRF33_01B replicated better in activated whole peripheral blood mononuclear cells (PBMCs) and CD4+ T-lymphocytes, but not monocyte-derived macrophages (MDMs). Also, its acquired fitness was greater than CRF01_AE but not subtype B. Moreover, CRF33_01B has higher rate of apoptotic cell death and syncytia induction compared to subtype B. These adaptive and survival abilities could have been acquired by CRF33_01B due to the incorporation of subtype B fragments into the gag-RT region of its full-length genome. Our studies confirm the previously held belief that HIV-1 strains may harbor enhanced biological fitness upon recombination. We therefore estimate a possible gradual replacement of the current predominance of CRF01_AE, as well as wider dissemination of CRF33_01B, together with the identification of other new CRF01_AE/B inter-subtype recombinants in Malaysia.
Fulltext First report of cervicofacial lymphadenitis due to Mycobacterium haemophilum in an immunocompromised adult patient

Atiya N, Sulaiman H, Chong J, Ng KP

J Infect Dev Ctries, 2015 Mar;9(3):313-6.
PMID: 25771471 DOI: 10.3855/jidc.5208

We report the first case of an immunocompromised adult patient presenting with cervicofacial lymphadenitis due to Mycobacterium haemophilum, confirmed using hsp65 gene sequencing and line-probe assays. In resource-limited settings, especially in developing countries, appropriate culture methods and rapid molecular diagnostic tools such as hsp65 gene sequencing for identification of this organism may not be readily available. This may cause M. haemophilum infections to go unrecognised or lead to delays in diagnosis. Lack of heightened awareness about the potential for this mycobacterial species to cause infections may also contribute to possible underestimation of M. haemophilum cases in the developing world.
Fulltext Fusarium sp. infection in a patient with acute lymphoblastic leukaemia

Tan R, Ng KP, Gan GG, Na SL

Med J Malaysia, 2013 Dec;68(6):479-80.
PMID: 24632920 MyJurnal

In the past two decades, Fusarium species have been increasingly recognized as serious pathogens in immunocompromised patients. The outcome of fusariosis in the context of severe persistent neutropaenia has been almost universally fatal. The treatment of fusariosis in immunocompromised patients remains a challenge and the prognosis of systemic fusariosis in this population remains poor. This report presents a case of fatal fusariosis in a 37- year-old patient who was diagnosed with precursor-B cell Acute Lymphoblastic Leukaemia (ALL).
Gene expression changes in human bronchial epithelial cells (BEAS-2B) and human pulmonary alveolar epithelial cells (HPAEpiC) after interaction with Cladosporium sphaerospermum

Lo SG, Wong SF, Mak JW, Choo KK, Ng KP

Med Mycol, 2020 Apr 01;58(3):333-340.
PMID: 31309220 DOI: 10.1093/mmy/myz061

Cladosporium is one of the most abundant spore. Fungi of this genus can cause respiratory allergy and intrabronchial lesion. We studied the differential expression of host genes after the interaction of Cladosporium sphaerospermum conidia with Human Bronchial Epithelial Cells (BEAS-2B) and Human Pulmonary Alveolar Epithelial Cells (HPAEpiC). C. sphaerospermum conidia were harvested and co-cultured with BEAS-2B cells or HPAEpiC cells for 48 hours respectively. This culture duration was chosen as it was associated with high germination rate. RNA was extracted from two biological replicates per treatment. RNA of BEAS-2B cells was used to assess changes in gene expression using AffymetrixGeneChip® Human Transcriptome Array 2.0. After co-culture with Cladosporium spores, 68 individual genes were found differentially expressed (P ≤ 0.05) and up-regulated ≥ 1.5 folds while 75 genes were found differentially expressed at ≤ -1.5 folds compared with controls. Reverse transcription and qPCR were performed on the RNA collected from both BEAS-2B cells and HPAEpiC cells to validate the microarray results with 7 genes. Based on the findings, infected pulmonary epithelial cells exhibited an increase in cell death-related genes and genes associated with innate immunity.
Genetic diversity, antifungal susceptibility and enzymatic characterisation of Malaysian clinical isolates of Candida glabrata

Lotfalikhani A, Khosravi Y, Sabet NS, Na SL, Ng KP, Tay ST

Trop Biomed, 2018 Dec 01;35(4):1123-1130.
PMID: 33601859

Candida glabrata has been reported as the second or third most common yeast species isolated from patients with vaginitis and invasive candidiasis. This study was aimed to determine the genetic diversity, antifungal susceptibility and enzymatic profiles of C. glabrata isolated from vaginal and blood samples in the Medical Microbiology Diagnostic Laboratory, University Malaya Medical Centre. A random amplified polymorphic DNA (RAPD) analysis method, using M13 and (GTG)5 primers, was used for strain differentiation of C. glabrata isolates. Antifungal susceptibility testing of C. glabrata isolates was determined using E-test against amphotericin B, caspofungin, fluconazole and voriconazole and microbroth dilution method against clotrimazole. The enzymic profiles of C. glabrata were determined using APIZYM semi-quantitation kit and egg-yolk agar method. A total of 14 RAPD patterns were identified amongst C. glabrata isolates investigated this study. Susceptibility to amphotericin B, caspofungin, fluconazole and voriconazole was noted. Approximately one third of the isolates demonstrated resistance to clotrimazole (MIC>=1 µg/ml). A single isolate of C. glabrata was resistant to caspofungin (MIC:1.5 µg/ml). Enzymatic activities of acid and alkaline phosphatase, aminopeptidases, esterase and lipase and phospholipase were detected in the C. glabrata isolates. The genetic diversity and antifungal susceptibility profiles of C. glabrata isolates were presented in this study. Continued surveillance and monitoring of the incidence and antifungal resistance in C. glabrata isolates is necessary.
Genetic relatedness of Candida strains isolated from women with vaginal candidiasis in Malaysia

Chong PP, Lee YL, Tan BC, Ng KP

J Med Microbiol, 2003 Aug;52(Pt 8):657-66.
PMID: 12867559

The aims of this study were to compare the genetic relatedness of: (i) sequential and single isolates of Candida strains from women with recurrent vaginal candidiasis (RVC); and (ii) Candida strains from women who had only one episode of infection within a 1-year period. In total, 87 isolates from 71 patients were cultured, speciated and genotyped by random amplification of polymorphic DNA (RAPD) analysis. Patients were categorized into three groups, namely those with: (i) a history of RVC from whom two or more yeast isolates were obtained (group A); (ii) a history of RVC from whom only a single isolate was obtained (group B); and (iii) a single episode of vaginal candidiasis within a 1-year period (group C). Six yeast species were detected: Candida albicans, Candida glabrata, Candida lusitaniae, Candida famata, Candida krusei and Candida parapsilosis. Interestingly, the prevalence of non-albicans species was higher in group A patients (50 %) than in patients in groups B (36 %) or C (18.9 %). Eighty RAPD profiles were observed, with a total of 61 polymorphic PCR fragments of distinct sizes. Clustering analysis showed that, overall, the majority of patients in group A had recurrent infections caused by highly similar, but not identical, sequential strains [mean pairwise similarity coefficient (S(AB)) = 0.721 +/- 0.308]. The range of mean S(AB) values for intergroup comparisons for C. albicans isolates alone was 0.50-0.56, suggesting that there was no significant relatedness between strains from different groups. Genetic similarity of C. albicans isolates from patients in group A was lower than that of C. albicans isolates from patients in group C (mean S(AB) = 0.532 +/- 0.249 and 0.636 +/- 0.206, respectively); this difference was statistically significant (P = 0.036). These results demonstrate that the cause of recurrent infections varies among individuals and ranges between strain maintenance, strain microevolution and strain replacement; the major scenario is strain maintenance with microevolution. They also show that C. albicans strains that cause recurrent infections are less similar to each other than strains that cause one-off infections, suggesting that the former may represent more virulent subtypes.
Fulltext Genome Analysis of the First Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance

Kuan CS, Chan CL, Yew SM, Toh YF, Khoo JS, Chong J, et al.

PLoS One, 2015;10(6):e0131694.
PMID: 26110649 DOI: 10.1371/journal.pone.0131694

The outbreak of extensively drug-resistant tuberculosis (XDR-TB) has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia.
Fulltext Genome Anatomy of Pyrenochaeta unguis-hominis UM 256, a Multidrug Resistant Strain Isolated from Skin Scraping

Toh YF, Yew SM, Chan CL, Na SL, Lee KW, Hoh CC, et al.

PLoS One, 2016;11(9):e0162095.
PMID: 27626635 DOI: 10.1371/journal.pone.0162095

Pyrenochaeta unguis-hominis is a rare human pathogen that causes infection in human skin and nail. P. unguis-hominis has received little attention, and thus, the basic biology and pathogenicity of this fungus is not fully understood. In this study, we performed in-depth analysis of the P. unguis-hominis UM 256 genome that was isolated from the skin scraping of a dermatitis patient. The isolate was identified to species level using a comprehensive multilocus phylogenetic analysis of the genus Pyrenochaeta. The assembled UM 256 genome has a size of 35.5 Mb and encodes 12,545 putative genes, and 0.34% of the assembled genome is predicted transposable elements. Its genomic features propose that the fungus is a heterothallic fungus that encodes a wide array of plant cell wall degrading enzymes, peptidases, and secondary metabolite biosynthetic enzymes. Antifungal drug resistance genes including MDR, CDR, and ERG11/CYP51 were identified in P. unguis-hominis UM 256, which may confer resistance to this fungus. The genome analysis of P. unguis-hominis provides an insight into molecular and genetic basis of the fungal lifestyles, understanding the unrevealed biology of antifungal resistance in this fungus.

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